User: lanhuong

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lanhuong20
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Posts by lanhuong

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Comment: C: Why DESeq2 gives large logfold for group with all zero count?
... Wouldn't this mean that all groups share the same intercept? I am interested in the effect (slope) of the variable x in each group, and each group should be allowed to have dissimilar mean (intercept).   ...
written 2.4 years ago by lanhuong20
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Comment: C: Why DESeq2 gives large logfold for group with all zero count?
... Thank you for a quick response! I found that including the term Timepoint first would give me the correct ordering: dsgn <- ~1 + Batch + Timepoint + Group + Timepoint:Group + Timepoint:Group:X My full column names for the design matrix would be (DESeq2::resultsNames(dds)): [1] "Intercept" ...
written 2.4 years ago by lanhuong20
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Why DESeq2 gives large logfold for group with all zero count?
... I have a following issue when running DESeq2 with a continuous effect variable. In my experiment there are 2 time points and 2 groups. Each sample (individual) has a sample at timepoint 1 and timepoint 2, but belongs to only one of the groups. dsgn <- "~1 + Batch + Group + Timepoint + Timepoin ...
microbiome deseq2 differential gene expression 16s written 2.4 years ago by lanhuong20
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Answer: A: [Limma] Testing continuous variable with interaction
... Thank you very much for a thorough response! Things are much clearer now. The reason I have multiple samples from the same subject per time point is that they are biological replicates taken at different days. So there are actually more than 2 time points. That is, samples are taken at a baseline t ...
written 3.2 years ago by lanhuong20 • updated 3.2 years ago by Ryan C. Thompson7.4k
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[Limma] Testing continuous variable with interaction
... Hi, I have a diet study experiment, where I would like to test whether a continuous variable, cont.var,  is related with gene expression data.  1) I would like to find the effect of cont.var  within each category (GroupA/GroupB), and within each time-point (T0/T1). The gene expression data was col ...
limma voom interactions confounding continuous written 3.2 years ago by lanhuong20
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Answer: A: What does DESeq2 rlog() return exactly?
... Hi,  So to make sure I understand all the steps correctly, since the part on rlog in DESEq2 paper is a bit short. Is this the sequence of operations done by rlog? 1. Matrix of initial LFC estimates is computed as M_ij = log_2 (K_ij/s_j + 1/2) / mean_j (K_ij/s_j + 1/2)  for all i and j. 2. The pri ...
written 3.7 years ago by lanhuong20
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What does DESeq2 rlog() return exactly?
... In the documentation or the rlog() function we can find that rlog(K_ij) = log2(q_ij) = beta_i0 + beta_ij, Which means the function would return the log2 transformed data after normalization by a size factor, estimating dispersion, shrinking dispersion and then the the beta parameters. Following t ...
deseq2 rlog rlog transformation written 3.7 years ago by lanhuong20

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Popular Question 2.4 years ago, created a question with more than 1,000 views. For What does DESeq2 rlog() return exactly?

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